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Hachem S, Yehya A, El Masri J, Mavingire N, Johnson JR, Dwead AM, Kattour N, Bouchi Y, Kobeissy F, Rais-Bahrami S, Mechref Y, Abou-Kheir W, Woods-Burnham L. Contemporary Update on Clinical and Experimental Prostate Cancer Biomarkers: A Multi-Omics-Focused Approach to Detection and Risk Stratification. BIOLOGY 2024; 13:762. [PMID: 39452071 PMCID: PMC11504278 DOI: 10.3390/biology13100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/11/2024] [Accepted: 09/20/2024] [Indexed: 10/26/2024]
Abstract
Prostate cancer remains a significant health challenge, being the most prevalent non-cutaneous cancer in men worldwide. This review discusses the critical advancements in biomarker discovery using single-omics and multi-omics approaches. Multi-omics, integrating genomic, transcriptomic, proteomic, metabolomic, and epigenomic data, offers a comprehensive understanding of the molecular heterogeneity of prostate cancer, leading to the identification of novel biomarkers and therapeutic targets. This holistic approach not only enhances the specificity and sensitivity of prostate cancer detection but also supports the development of personalized treatment strategies. Key studies highlighted include the identification of novel genes, genetic mutations, peptides, metabolites, and potential biomarkers through multi-omics analyses, which have shown promise in improving prostate cancer management. The integration of multi-omics in clinical practice can potentially revolutionize prostate cancer prognosis and treatment, paving the way for precision medicine. This review underscores the importance of continued research and the application of multi-omics to overcome current challenges in prostate cancer diagnosis and therapy.
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Affiliation(s)
- Sana Hachem
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Amani Yehya
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Jad El Masri
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Nicole Mavingire
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
| | - Jabril R. Johnson
- Department of Microbiology, Biochemistry, & Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
| | - Abdulrahman M. Dwead
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
| | - Naim Kattour
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Yazan Bouchi
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Firas Kobeissy
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Soroush Rais-Bahrami
- Department of Urology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Leanne Woods-Burnham
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
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Capitanio U, Autorino R, Bandini M, Briganti A, Cheng L, Cooperberg MR, Dehò F, Gallina A, Klotz L, Lane B, Montironi R, Salonia A, Stief C, Tombal B, Montorsi F. Incidental Prostate Cancer (cT1a-cT1b) Is a Relevant Clinical and Research Entity and Should Be Fully Discussed in the International Prostate Cancer Guidelines. Eur Urol Oncol 2021; 5:S2588-9311(21)00049-3. [PMID: 33814342 DOI: 10.1016/j.euo.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/06/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Affiliation(s)
- Umberto Capitanio
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Marco Bandini
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alberto Briganti
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew R Cooperberg
- Departments of Urology and Epidemiology & Biostatistics, Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
| | - Federico Dehò
- Unit of Urology, Ospedale ASST Sette Laghi, Varese, Italy
| | - Andrea Gallina
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Laurence Klotz
- Division of Urology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - Brian Lane
- Department of Surgery, Michigan State University College of Human Medicine, Grand Rapids, MI, USA; Division of Urology, Spectrum Health Hospital System, Grand Rapids, MI, USA
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, United Hospitals, Ancona, Italy
| | - Andrea Salonia
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Christian Stief
- Department of Urology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Bertrand Tombal
- Service d'Urologie, Cliniques universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Francesco Montorsi
- Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy; Division of Experimental Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy.
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Abstract
BACKGROUND Embedding techniques for converting high-dimensional sparse data into low-dimensional distributed representations have been gaining popularity in various fields of research. In deep learning models, embedding is commonly used and proven to be more effective than naive binary representation. However, yet no attempt has been made to embed highly sparse mutation profiles into densely distributed representations. Since binary representation does not capture biological context, its use is limited in many applications such as discovering novel driver mutations. Additionally, training distributed representations of mutations is challenging due to a relatively small amount of available biological data compared with the large amount of text corpus data in text mining fields. METHODS We introduce Mut2Vec, a novel computational pipeline that can be used to create a distributed representation of cancerous mutations. Mut2Vec is trained on cancer profiles using Skip-Gram since cancer can be characterized by a series of co-occurring mutations. We also augmented our pipeline with existing information in the biomedical literature and protein-protein interaction networks to compensate for the data insufficiency. RESULTS To evaluate our models, we conducted two experiments that involved the following tasks: a) visualizing driver and passenger mutations, b) identifying novel driver mutations using a clustering method. Our visualization showed a clear distinction between passenger mutations and driver mutations. We also found driver mutation candidates and proved that these were true driver mutations based on our literature survey. The pre-trained mutation vectors and the candidate driver mutations are publicly available at http://infos.korea.ac.kr/mut2vec . CONCLUSIONS We introduce Mut2Vec that can be utilized to generate distributed representations of mutations and experimentally validate the efficacy of the generated mutation representations. Mut2Vec can be used in various deep learning applications such as cancer classification and drug sensitivity prediction.
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Affiliation(s)
- Sunkyu Kim
- Department of Computer Science and Engineering, Korea University, Seoul, Korea
| | - Heewon Lee
- Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea
| | - Keonwoo Kim
- Department of Computer Science and Engineering, Korea University, Seoul, Korea
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University, Seoul, Korea. .,Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
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Shah RB, Yoon J, Liu G, Tian W. Atypical intraductal proliferation and intraductal carcinoma of the prostate on core needle biopsy: a comparative clinicopathological and molecular study with a proposal to expand the morphological spectrum of intraductal carcinoma. Histopathology 2017; 71:693-702. [DOI: 10.1111/his.13273] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/30/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Rajal B Shah
- Division of Pathology; Miraca Life Sciences; Irving TX USA
- Department of Pathology; Baylor College of Medicine; Houston TX USA
| | - Jiyoon Yoon
- Division of Pathology; Miraca Life Sciences; Irving TX USA
| | - Gang Liu
- University of Toledo; Toledo OH USA
| | - Wei Tian
- Division of Pathology; Miraca Life Sciences; Irving TX USA
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Cheng L, Zhang S, Wang L, MacLennan GT, Davidson DD. Fluorescence in situ hybridization in surgical pathology: principles and applications. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2017; 3:73-99. [PMID: 28451457 PMCID: PMC5402181 DOI: 10.1002/cjp2.64] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 02/06/2023]
Abstract
Identification of recurrent tumour‐specific chromosomal translocations and novel fusion oncogenes has important diagnostic, therapeutic and prognostic implications. Over the past decade, fluorescence in situ hybridization (FISH) analysis of tumour samples has been one of the most rapidly growing areas in genomic medicine and surgical pathology practice. Unlike traditional cytogenetics, FISH affords a rapid analysis of formalin‐fixed, paraffin‐embedded cells within a routine pathology practice workflow. As more diagnostic and treatment decisions are based on results of FISH, demand for the technology will become more widespread. Common FISH‐detected alterations are chromosome deletions, gains, translocations, amplifications and polysomy. These chromosome alterations may have diagnostic and therapeutic implications for many tumour types. Integrating genomic testing into cancer treatment decisions poses many technical challenges, but rapid progress is being made to overcome these challenges in precision medicine. FISH assessment of chromosomal changes relevant to differential diagnosis and cancer treatment decisions has become an important tool for the surgical pathologist. The aim of this review is to provide a theoretical and practical survey of FISH detected translocations with a focus on strategies for clinical application in surgical pathology practice.
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Affiliation(s)
- Liang Cheng
- Department of Pathology and Laboratory MedicineIndiana University School of MedicineIndianapolisINUSA.,Department of UrologyIndiana University School of MedicineIndianapolisINUSA
| | - Shaobo Zhang
- Department of Pathology and Laboratory MedicineIndiana University School of MedicineIndianapolisINUSA
| | - Lisha Wang
- Michigan Center for Translational PathologyUniversity of MichiganAnn ArborMIUSA
| | - Gregory T MacLennan
- Departments of Pathology and Laboratory MedicineCase Western Reserve UniversityClevelandOHUSA
| | - Darrell D Davidson
- Department of Pathology and Laboratory MedicineIndiana University School of MedicineIndianapolisINUSA
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